I don't think I've ever felt like it's OK for my program to provide a list of answers where some are right and some are wrong, but reading this... and generally believing in P != NP.... maybe that's a decent way of looking at some stuff!
If so, the language they thought they were using (and that they should actually use) is datalog, not prolog.
Datalog has declarative semantics: All facts that are derivable from the base database and the rules will be derived by the interpreter, and it will not add extra hallucinated facts. If that's not true, it's a bug in the runtime, not in the language.
But you can use it for lots of things. Whenever I'm frustrated with graph based tools being slow (like build systems), I run the graph through a datalog engine for comparison. It's usually much, much faster.